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genechip microarray analysis suite 5.0  (Thermo Fisher)


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    Thermo Fisher genechip microarray analysis suite 5.0
    Genechip Microarray Analysis Suite 5.0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/genechip+microarray+analysis/pmc03359358-62-9-14
    Average 90 stars, based on 1 article reviews
    genechip microarray analysis suite 5.0 - by Bioz Stars, 2026-10
    90/100 stars

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    other:

    Article Title: Production and characterization of amplified tumor-derived cRNA libraries to be used as vaccines against metastatic melanomas
    Article Snippet: According to the Microarray Analysis Suite 5.0 software (MAS 5.0; Affymetrix), 34% and 36% of the genes that were reported as "present" in the tumor total RNA were also detected as "present" in the amplified libraries of patients MEL02 and MEL10 respectively (Theses transcripts are qualified as "recovered" in the following).

    Article Title: Alteration of gene expression by alcohol exposure at early neurulation
    Article Snippet: The data from independent arrays (each with RNA from a single embryo) for each of the treatments were extracted using the Affymetrix Microarray Suite 5.0 (MAS5) algorithm.

    Article Title: Transcriptional signature of an adult brain tumor in Drosophila
    Article Snippet: The single arrays were analysed using Microarray Suite 5.0 (Affymetrix).

    Article Title: Conserved Transcriptional Regulatory Programs Underlying Rice and Barley Germination
    Article Snippet: The most unreliable data with absent call across 9 chips based on analyzed result using Microarray Suite 5.0 (Affymetrix, Santa Clara, CA) were filtered out.

    Article Title: Production and characterization of amplified tumor-derived cRNA libraries to be used as vaccines against metastatic melanomas
    Article Snippet: Scanned images were processed using the Microarray Analysis Suite 5.0 (MAS 5.0; Affymetrix) and expression differences between tumor and library samples were determined by baseline comparison algorithms provided by the software.

    Article Title: The effect of oxythioquinox exposure on normal human mammary epithelial cell gene expression: A microarray analysis study
    Article Snippet: Expression profiles were analyzed using Microarray Suite 5.0, MicroDB 3.0 and Data Mining Tool 3.0 (Affymetrix).

    Microarray:

    Article Title: Reproducibility of gene expression across generations of Affymetrix microarrays
    Article Snippet: .. The analysis was repeated using the Affymetrix Microarray Suite 5.0 (MAS 5.0). .. Affymetrix software also assigns every probe set an "absolute call" (Present [P], Absent [A], Marginal [M]), which represents a qualitative indication of whether or not a transcript is detected within a sample.

    Article Title: A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"
    Article Snippet: Expression values for all genes within the Arabidopsis genome present on the Affymetrix chip were taken from published data on nitrogen treatments vs. controls for all the available experiments from the data sets published in:[ - , ]. .. All microarray data used in this analysis was processed and normalized using Affymetrix Suite 5.0 or MAS5 Software (as implemented in the R statistical package [ ] the two normalization Methods gave equivalent results. ..

    Software:

    Article Title: A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"
    Article Snippet: Expression values for all genes within the Arabidopsis genome present on the Affymetrix chip were taken from published data on nitrogen treatments vs. controls for all the available experiments from the data sets published in:[ - , ]. .. All microarray data used in this analysis was processed and normalized using Affymetrix Suite 5.0 or MAS5 Software (as implemented in the R statistical package [ ] the two normalization Methods gave equivalent results. ..



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    Graphs showing the representative transcripts of genes related to vitamin A metabolism in qRT-PCR. QRT-PCR was also performed for the genes AKR1B15, RDH12, AKR1B10, and CRABP2, which are upregulated more than twentyfold among the significantly upregulated genes and promote binding to RAR, two genes (RARB and RARRES3) whose expression was downregulated more than 1/50, and RARA and RARG, which are other types of RAR. By normalizing the expression of the gene of interest to the expression of 18S rRNA, we were able to obtain a relative measure of the expression level of each gene (* P < 0.05, ** P < 0.005, *** P < 0.0005). Similar to the <t>microarray</t> results, RARB, CRABP2, and RARRES3 showed significant differences, whereas RARA and RARG showed no significant differences.
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    Graphs showing the representative transcripts of genes related to vitamin A metabolism in qRT-PCR. QRT-PCR was also performed for the genes AKR1B15, RDH12, AKR1B10, and CRABP2, which are upregulated more than twentyfold among the significantly upregulated genes and promote binding to RAR, two genes (RARB and RARRES3) whose expression was downregulated more than 1/50, and RARA and RARG, which are other types of RAR. By normalizing the expression of the gene of interest to the expression of 18S rRNA, we were able to obtain a relative measure of the expression level of each gene (* P < 0.05, ** P < 0.005, *** P < 0.0005). Similar to the microarray results, RARB, CRABP2, and RARRES3 showed significant differences, whereas RARA and RARG showed no significant differences.

    Journal: Investigative Ophthalmology & Visual Science

    Article Title: Alteration of Gene Expression in Pathological Keratinization of the Ocular Surface

    doi: 10.1167/iovs.65.6.37

    Figure Lengend Snippet: Graphs showing the representative transcripts of genes related to vitamin A metabolism in qRT-PCR. QRT-PCR was also performed for the genes AKR1B15, RDH12, AKR1B10, and CRABP2, which are upregulated more than twentyfold among the significantly upregulated genes and promote binding to RAR, two genes (RARB and RARRES3) whose expression was downregulated more than 1/50, and RARA and RARG, which are other types of RAR. By normalizing the expression of the gene of interest to the expression of 18S rRNA, we were able to obtain a relative measure of the expression level of each gene (* P < 0.05, ** P < 0.005, *** P < 0.0005). Similar to the microarray results, RARB, CRABP2, and RARRES3 showed significant differences, whereas RARA and RARG showed no significant differences.

    Article Snippet: Microarray experiments were then performed according to the protocols provided by Thermo Fisher Scientific, and scanned microarray images were obtained using the GeneChip Scanner 3000 7G (Thermo Fisher Scientific) microarray analysis system.

    Techniques: Quantitative RT-PCR, Binding Assay, Expressing, Microarray